Fig. 2: Reclassification of the PAM50 Normal-like subtype and characterization of the BCC Luminal subtype.

a Representative histological sections (H&E-stained) of samples annotated as PAM50 Normal-like, with adipose tissue and DCIS component present. Scale bar—500 μm. b Mean tumor content across reported PAM50 subtypes in TCGA (n = 1048) determined by WES. The color key included is used for (b), (c), and (d). ***: p value < 0.001, **: p value < 0.01, *: p value < 0.05, -: p value < 0.1. c Gene expression levels in the adipose signature (in scaled SSGSEA scores) across reported PAM50 subtypes and normal tissue. d Gene expression levels in the proliferation signature across reported PAM50 subtypes and normal tissue. e Sankey plot depicting the distribution of PAM50 Normal-like samples between BCC LumA and LumB subtypes and among the IHC-defined phenotypes. f Kaplan–Meier survival curves for the PAM50 and BCC LumA/LumB subtypes. g Delineation of the SCAN-B Luminal subtype into LumA and LumB with the BCC using proliferative and anti-proliferative signatures as explanatory variables. The blue line reflects the proposed threshold of signature scores between LumA and LumB. h Barplots showing the distribution of KI67-positive samples between PAM50 LumA/LumB subtypes. i Barplots showing the distribution of KI67-positive samples across BCC LumA/LumB subtypes. j Cox proportional hazard regression analysis showing the change of survival rates across the BCC LumB/LumA subtypes in the METABRIC cohort (top) depending on additional variables: stage (middle) and molecular grade (bottom). HR Hazard ratio; CI confidence interval.